Documentation gap: recommended SV caller for this tool? Specific format, but no tools suggested.

[jamesdalg]

If I might ask, what tool is used to generate a VCF with INFO fields as the README suggests?

It's not documented anywhere that I can see.

[xuefzhao]

Thank you for your interest in our tool!

For canonical SVs, the standard VCF 4.1 format should serve as a suitable input. However, for complex SVs, the examples provided were adapted from the outputs of tools such as GATK-SV and SVelter. Since different algorithms may represent complex SVs in varying formats, we do not provide scripts to standardize VCF input. Instead, we have shared example files to illustrate the expected format, and users are encouraged to create their own scripts to adapt their data accordingly.

I’d be happy to assist or provide guidance in formatting your SV calls to ensure compatibility with our tool. Please feel free to reach out if you need further clarification or support.